Episode 10: Returning Legend

Welcome back to the blog, we will first begin with the dankest of memes. Today I have the legendary rapper Yung Lean. Lean rose to fam with his bucket hats, AZ iced tea, and general meme filled raps. An example is a line from Kyoto, "I got an empire of emotional, Squad see me crusin', crusin' in my go kart, I'm War ho, I'm Warhol, I'm Wario when I'm in Mario Kart" Although he is now far removed from his meme days, he is still a figure within the dank community.

My methodology will be pretty chill probably. I gonna start off by preparing LacI with several different mutations determined from other studies I've looked at. Then I'll run an REMD simulation on these proteins, simulating the mutated protein at several different temperatures. REMD is just the program I will be using. After that, I will introduce a random brownian kick which will send a reaction wave down the molecule. After the wave is sent through the molecule, I will use a DFI analysis to evaluate the change of molecule positioning. Then I plan to define what changes I am looking for in order to better understand the procedure. It shouldn't be too bad, but who knows anything is possible at this point.

But I am also looking to include a lay audience so I will have to avoid many of the pitfalls of the research papers I have read, which includes technical language, reliance on credentials, no limitation discussion, and a lack of explanation and justification.

Overall, I am very confident in my method because it is similar to one of my professor's papers. The random brownian kick and DFI analysis will help me analyze the reactions of the LacI protein. Hopefully i will be able to obtain meaningful results. However, I will have to justify and explicate the methods thoroughly because the technical information can bog down the reader and hurt the understanding of the project. I am also unsure of what I am going to define as a "significant change" within the protein structure. I will have to consult with my PSF 3rd floor professor because she has a good understanding of the changes in protein functionality. I am also unsure of the timeline required for my project, but I am sure the data will be collected in a timely fashion. Another challenge I face is converting technical terms into readable sentences for the everyday man. I hope to correct the short comings of science professors with an understandable paper.

Episode 9: MIA 2 months

What is actually happened after I redid my sources

Hello fam, I'm back after not blogging for like a solid month and a half. And of course I am bringing the dankest of memes. Today I have the one the only living legend, Filthy Frank. Filthy Frank is a legendary internet superstar. He is the person who started the Harlem Shake, but he is also responsible for many diverse and very dank memes with topics ranging from Japan to Vegans.

My literature review was the solving of what seemed to be endless doubts. At the beginning of the process I'll admit to being very cocky. The topics I initially researched were on the general topic of protein folding, but not actually on the focus of mechanisms. And I never really realized it until I met with my Professor, Dr. Ozkan PSF 3rd Floor Fam. I had been focusing too much on some unfolding techniques I heard vaguely before in my lab and I left out some of the basic biology required to understand my topic. So for my annotated bibliography I scrapped a solid 14 sources, and found new ones, resulting in a completed base for my literature review. This was probably one of the hardest parts of the project because creating the foundation of my research is the most abstract task in AP Research. For similar reasons my first outline almost no relation to my final outline, which is probably why it was better. The outline was one of the highlights of the first trimester. I finished that thing hours before the deadline and slept well before the due date. It included around 4k words and plenty of depth into protein folding.

Ozkan when she saw the first outline

When cutting down the outline, many subtopics were cut out. This narrowed the focus of the literature review, saving the word count and the methods section. Writing the literature review really helped me translate my ideas for a general audience. Although I knew what I would be doing in my research, I did not know how to grasp the literature surrounding my topics. The whole process of the lit review helped me understand the concepts behind protein folding.

With the base of all my research completed, it is now time to shift into second gear and tackle the methods section. I am pretty confident about my methods section, as I know what I am going to pursue. However, the details need to be ironed out and I have to understand all the programs I am going to be using. Now that the most difficult task is over, it is now time to complete the second hardest section of my research paper, the methods.

TIME TO STOP PANICKING